8QRE

Cholera holotoxin (wildtype)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Using Vibrio natriegens for High-Yield Production of Challenging Expression Targets and for Protein Perdeuteration.

Mojica, N.Kersten, F.Montserrat-Canals, M.Huhn Iii, G.R.Tislevoll, A.M.Cordara, G.Teter, K.Krengel, U.

(2024) Biochemistry 63: 587-598

  • DOI: https://doi.org/10.1021/acs.biochem.3c00612
  • Primary Citation of Related Structures:  
    8QRE

  • PubMed Abstract: 

    Production of soluble proteins is essential for structure/function studies; however, this usually requires milligram amounts of protein, which can be difficult to obtain with traditional expression systems. Recently, the Gram-negative bacterium Vibrio natriegens emerged as a novel and alternative host platform for production of proteins in high yields. Here, we used a commercial strain derived from V. natriegens (Vmax X2) to produce soluble bacterial and fungal proteins in milligram scale, which we struggled to achieve in Escherichia coli . These proteins include the cholera toxin (CT) and N -acetyl glucosamine-binding protein A (GbpA) from Vibrio cholerae , the heat-labile enterotoxin (LT) from E. coli and the fungal nematotoxin CCTX2 from Coprinopsis cinerea . CT, GbpA, and LT are secreted by the Type II secretion system in their natural hosts. When these three proteins were produced in Vmax, they were also secreted and could be recovered from the growth media. This simplified the downstream purification procedure and resulted in considerably higher protein yields compared to production in E. coli (6- to 26-fold increase). We also tested Vmax for protein perdeuteration using deuterated minimal media with deuterium oxide as solvent and achieved a 3-fold increase in yield compared to the equivalent protocol in E. coli . This is good news, since isotopic labeling is expensive and often ineffective but represents a necessary prerequisite for some structural biology techniques. Thus, Vmax represents a promising host for production of challenging expression targets and for protein perdeuteration in amounts suitable for structural biology studies.


  • Organizational Affiliation

    Department of Chemistry, University of Oslo, NO-0315 Blindern, Oslo, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cholera enterotoxin subunit AA,
G [auth B]
240Vibrio cholerae O1Mutation(s): 0 
Gene Names: ctxA
UniProt
Find proteins for P01555 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P01555 
Go to UniProtKB:  P01555
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01555
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cholera enterotoxin subunit B103Vibrio cholerae O1Mutation(s): 2 
Gene Names: ctxBtoxBVC_1456
UniProt
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P01556 
Go to UniProtKB:  P01556
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01556
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLA
Query on GLA

Download Ideal Coordinates CCD File 
IA [auth C]alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
GAL
Query on GAL

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AA [auth G]
CA [auth H]
KA [auth I]
N [auth A]
NA [auth J]
AA [auth G],
CA [auth H],
KA [auth I],
N [auth A],
NA [auth J],
PA [auth K],
QA [auth L],
S [auth D],
U [auth E],
X [auth F]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
Y [auth G]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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BA [auth G]
DA [auth H]
GA [auth B]
JA [auth C]
LA [auth I]
BA [auth G],
DA [auth H],
GA [auth B],
JA [auth C],
LA [auth I],
MA [auth I],
O [auth A],
OA [auth J],
P [auth A],
Q [auth A],
RA [auth L],
SA [auth L],
T [auth D],
V [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

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HA [auth C],
W [auth F],
Z [auth G]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

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EA [auth B],
FA [auth B],
M [auth A],
R [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.659α = 90
b = 108.128β = 95.958
c = 124.765γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR03AI112854
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI137056

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release